I was wondering how all this panned out- did it get resolved? What was the problem?
I'm experiencing pretty much the same with my todays installation of new HDX system and PT12HD on Mac tower with both OSX10.10 and 10.11. Card is seen in OSX as a pcie card but not seen by Protools. Moving card to different slot doesn't change anything.

Just a word of warning: do not put an HDX card in a 2008 Mac Pro. if you start/install a Pro Tools version that requires a firmware update of the HDX card (many of the versions do), it will brick the card. That's the real big problem with putting those cards in Harpertown/Penryn Mac Pro towers. If you happen to update the card first on a qualified computer and then move it to the 2008 Mac Pro, it'll work. Just don't do firmware updates.

On top of that, the HDX card won't be recognized by Pro Tools until the firmware update is at least the update that matches that Pro Tools version. For instance,

Install card, install HD driver and you see no HDX card.

Start Pro Tools.

Pro Tools will tell you it needs to update the firmware of the card.

Update the firmware.

Restart the computer.

Now the HDX card will show for both Pro Tools and macOS Audio MIDI Setup.